plantinfo <- read.csv("plantCodes_beans2017.csv",stringsAsFactors = F)
plantinfo <- plantinfo[plantinfo$batch==3,c("plantID","germinationDate","strain")]
plantinfo$germinationDate <- as.Date(plantinfo$germinationDate, format=c("%m/%d/%Y"))
yield <- read.table("seedMass_beansbatch3.txt",sep=",",header=T)
yield$plantID <- gsub(" ","",yield$plantID)
setdiff(yield$plantID,plantinfo$plantID)
b3yield <- merge(plantinfo, yield,by="plantID")

assaydata <- read.csv("H2assayOutput_batch3/batch3H2output.csv",stringsAsFactors = F)
str(assaydata)
##Based on looking at the data, it would make more sense to use the 
# CO2 measurement at the beginning of the O2 steps for specific N2 ase (instead
# of CO2 at peak H2)
## this is the intercept of the CO2 drift correction.
assaydata$specificN2ase_CO2 <- assaydata$H2ppm_Ar/assaydata$CO2drift_intercept
assaydata$plantID <- substr(assaydata$file,10,12)
assaydata$date <- substr(assaydata$file,1,8)
assaydata$date <- as.Date(assaydata$date,format=c("%Y%m%d"))
b3h2 <-  merge(assaydata,plantinfo,by="plantID")

#save(b3h2,b3yield,file="batch3_assayPlusSeedYieldEdited.RData")